Multi-species Occupancy Model Research Articles

Forest cover is more important than its integrity or landscape configuration in determining habitat use by mammals in a human-modified landscape in Colombia

Human activities shape the structure of landscapes in different ways and hence modify animal communities depending on the type and intensity of these activities. The Montes de Maria subregion of Colombia has experienced a heavy transformation of most areas despite covering one of the last remnants of dry forest, a critically endangered ecosystem. However, the effects of this transformation have been little explored. Here, we used a multispecies occupancy model (MSOM) to understand the relative influence of three components of land-use change – deforestation (remaining forest amount), degradation of forest integrity (forest quality) and fragmentation (landscape configuration) on mammalian habitat use across a mosaic of tropical dry forest in Colombia. Our data suggest that the percentage of forest cover was substantially important for herbivores, and consistently showed a moderate effect on the entire community and some individual species. High variability in species-specific responses to the examined variables hindered broad taxonomic generalizations, nevertheless, we detected a moderate positive effect of forest cover in both diet specialists and generalists species, as well as in species with small home ranges. Although omnivores responses, tended to use less complex landscapes (mosaics of land uses), there was high uncertainty in this response. The lack of substantial effects on most species, and the absence of threatened species across this anthropogenic landscape, suggests that the current community is composed of species tolerant to habitat modifications, but not only diet generalist species. This is most likely the result of a long filtering process caused by land use transformation and hunting which could have caused non-sensitive species to distribute relatively homogenously across this landscape. Our results suggest that conservation strategies in the study area should focus on conserving and expanding as much forest as possible rather than only improving the quality of already existing forest patches.

Interspecific interactions among major carnivores in Panna Tiger Reserve: A multispecies occupancy approach

AbstractLarge carnivores play a crucial role in trophic cascades, affecting the population dynamics of both co‐predators and prey within an ecosystem. Understanding the significance of these carnivores in trophic interactions is essential for developing effective conservation and management strategies. We examined the effects of occupancy dynamics and patterns of species interactions and coexistence within the carnivore guild in the Panna Tiger Reserve in India. We collected camera trap data (two seasons, 2019) in a presence–absence framework and applied multispecies occupancy models to assess the occupancy, co‐occurrence, and interactions among species. We also examined activity overlap to understand the temporal segregation in the carnivore guild. The mean marginal occupancy was highest for leopards in winter (Ψwinter 0.92 ± 0.02, Ψsummer 0.63 ± 0.05) and hyenas in summer (Ψsummer 0.93 ± 0.03, Ψwinter 0.78 ± 0.03) and was lowest for tigers in both seasons (Ψwinter 0.62 ± 0.05, Ψsummer 0.15 ± 0.05). Co‐occurrence probability among carnivores was higher in winter than in summer, and conditional occupancy was consistently higher when other species were present. Different environmental factors influenced marginal occupancy and co‐occurrence patterns across seasons. Strong temporal overlaps were recorded between tiger–leopard (0.87–0.91) and tiger–hyena (0.78–0.79). We detected a significant spatial segregation between tigers and leopards, as they prefer different habitat types in different seasons, along with high temporal overlap. Resource availability strongly governs the association of carnivores with their habitat selection. Hyenas demonstrated higher dependency on tigers than on leopards for resources. These findings indicate that coexistence with apex‐predator species is feasible through strategic adaptation to fulfill resource requisition.

Improving Inference Within Freshwater Community Studies: Accounting for Variable Detection Rates of Amphibians and Fish.

Research into freshwater communities often aims to link patterns of species distribution in ponds with underlying biotic factors. However, errors with species detection (e.g. false negatives) may underestimate distribution and bias assessments of community structure. Occupancy models that account for imperfect detection offer a solution to this problem. Here, we used three methods (call/visual encounter surveys, dip-netting and newt trapping) to survey amphibians and fish (potential amphibian predators) at 100 ponds in an urbanised landscape in Hungary over one breeding season. We estimated species detection probabilities for amphibians (all life stages combined) and fish using occupancy models to gain insight into amphibian-fish relationships and other survey-specific variables. We detected nine amphibian and 20 fish species. There were relatively low but variable estimated probabilities of detection for amphibians (mean: 0.320, 95% Bayesian credible interval: 0.142-0.598), with three species having detection rates < 0.1. Probabilities of detection peaked in the middle of the breeding season and increased with survey effort. Detection probabilities of five species were negatively associated with the detection of fish at a pond, while there were positive relationships between detection and emergent vegetation cover. We found no substantial differences in detection rates among the three survey methods. The probability of detecting fish was much higher than for amphibians (0.588, 0.503-0.717) but was lower at ponds with high emergent vegetation where amphibian detection was higher. Our results underscore the importance of accounting for the imperfect detection of both response organisms and potentially interacting species in aquatic community studies. We recommend applying multi-species occupancy models to enable inference for both common and rare species at ponds in landscapes subjected to human disturbances.

Wildlife resilience in an urban landscape: understanding land-use impacts in Cape Town

AbstractUrbanisation is rapidly transforming and fragmenting natural habitats, disrupting ecosystems and negatively impacting biodiversity. The City of Cape Town (CoCT) is situated in a global biodiversity hotspot, but sustained anthropogenic activities have resulted in the local extirpation of most medium and large mammals. A recent survey of mammals within urban protected areas of CoCT revealed that a few, mostly medium-sized generalist species, persist. It is uncertain which native mammal species, if any, inhabit the unprotected green belts and parks in suburban and urban areas of the city. A total of 37 camera trap sites were established along four transects for a period of four months between 31 January and 31 May 2022. A total of 12 terrestrial mammal species were detected, nine of which were wild native mammals and three domestic species. Most detections were in natural habitat followed by suburban, with urban areas having the lowest detection rate of wildlife. Single season hierarchical multi-species occupancy models revealed that tree cover had a significant positive effect on both community and individual species occupancy. Contrary to our predictions, neither human population density nor the extent of the impervious surface at sites significantly affected occupancy. Cape grysbok (Raphicerus melanotis) were significantly more likely to occur at sites with a higher proportion of impervious surfaces supporting other recent research, which showed this species together with water mongoose (Atilax paludinosus) and Cape porcupine (Hystrix africaeaustralis) are one of only a few native mammals that appear to persist and may even thrive in human-modified landscapes. Our findings underscore the complexity of urban biodiversity conservation and the species-specific responses to environmental factors, emphasising the importance of tree cover in urban wildlife management.

Collapse of invasive competitor expands distribution of endangered ecosystem engineer

Negative interactions among invasive predators, competitors and native species can often disrupt ecosystem services, particularly when keystone species are affected. The Key Largo woodrat (Neotoma floridana smalli) is an endangered ecosystem engineer, endemic to protected hammocks on the northern third of the island of Key Largo, FL, USA. Invasive predator control efforts have assisted in woodrat recovery, but less is known about how a potential competitor, the black rat (Rattus rattus), interacts with the woodrat. We conducted camera trap surveys at supplemental nest sites throughout the range of the woodrat and used multi-species occupancy models to investigate factors influencing woodrat and black rat co-occurrence. Supplemental nest sites were surveyed each year over a three-year period, during which the population of black rats within the protected hammock declined precipitously. Woodrats and black rats occurred at similar levels in the first survey with occupancy probabilities of 22.8 % and 15.6 %, respectively. Both species occurred at fewer sites in the second survey, but while woodrats later rebounded, black rats were only detected twice in the final survey. There was evidence of species avoidance between the rodents based on a species interaction term, and they exhibited opposing relationships with predictor variables of both detection and occupancy probabilities. As the occupancy of black rats decreased, the relationship between woodrats and distance from developed areas also weakened. Following the black rat decline, woodrats recolonized an area previously dominated by black rats, where they had been presumed extirpated for 2–3 decades. Our results indicate that black rat competition restricted occupancy of Key Largo woodrats, hindering recovery efforts that previously concentrated on invasive predator removal, demonstrating the need to consider influences of both invasive predators and competitors in species recovery programs.

An integrated assessment of niche partitioning reveals mechanisms of coexistence between mesocarnivores

Species diversity depends on the capacity of species to coexist, and when these share similar ecological requirements some degree of partitioning of the ecological niche is expected. Within the order Carnivora, direct and indirect interspecific interactions shape community structure and composition. Although strong negative interactions (e.g., interspecific killing) are expected between large carnivores and subordinate species, mesocarnivores that dominate most human disturbed landscapes can still strongly compete for resources given their similar body size and energy requirements. To identify the mechanisms of coexistence between mesocarnivore species in a Mediterranean landscape we assessed the ecological niche overlap between five species (Vulpes vulpes, Meles meles, Martes foina, Herpestes ichneumon, Genetta genetta), by simultaneously measuring the space, time, and trophic resource use. The multi-species occupancy model fit to camera-trapping data revealed spatial co-occurrence between most species’ pairs and an avoidance pattern between only stone marten and Eurasian badger (78 % probability of a negative effect). Using genetically identified scats, we assessed trophic niche breadth and overlap. Niche breadth was narrow for red fox, Eurasian badger, and stone marten, given these species consumed almost exclusively fruits and arthropods, and so trophic niche overlap was high. For the genet and the mongoose, the consumption of different food resources (e.g., mammals, birds, and reptiles) increased niche breadth and decreased the niche overlap with the other sympatric species. Finally, niche segregation was more significant along the temporal axis, since the mongoose has a diurnal activity pattern and the remaining carnivore species, although mostly nocturnal, had small asynchronies in the activity peaks which could decrease the chance of direct encounters. Therefore, our results suggest that similar habitat preferences and ecological requirements rather than interspecific competition shape the mesocarnivores’ resource use in this landscape. Nonetheless, fine-scale temporal segregation seems the main mechanism to facilitate coexistence, together with small differences in trophic resource use, especially for species with high spatial and temporal overlap.

Accounting for imperfect detection when estimating species-area relationships and beta-diversity.

Ecologists have historically quantified fundamental biodiversity patterns, including species-area relationships (SARs) and beta diversity, using observed species counts. However, imperfect detection may often bias derived community metrics and subsequent community models. Although several statistical methods claim to correct for imperfect detection, their performance in species-area and β-diversity research remains unproven. We examine inaccuracies in the estimation of SARs and β-diversity parameters that emerge from imperfect detection, and whether such errors can be mitigated using a non-parametric diversity estimator (iNEXT.3D) and Multi-Species Occupancy Models (MSOMs). We simulated 28,350 sampling regimes of 2835 fragmented communities, varying the mean and standard deviation of species detection probabilities, and the number of sampling repetitions. We then quantified the bias, accuracy, and precision of derived estimates of model coefficients for SARs and the effects of patch area on β-diversity (pairwise Sørensen similarity). Imperfect detection biased estimates of all evaluated parameters, particularly when mean detection probabilities were low, and there were few sampling repetitions. Observed counts consistently underestimated species richness and SAR z-values, and overestimated SAR c-values; iNEXT.3D and MSOMs only partially resolved these biases. iNEXT.3D provided the best estimates of SAR z-values, although MSOM estimates were generally comparable. All three methods accurately estimated pairwise Sørensen similarity in most circumstances, but only MSOMs provided unbiased estimates of the coefficients of models examining covariate effects on β-diversity. Even when using iNEXT.3D or MSOMs, imperfect detection consistently caused biases in SAR coefficient estimates, calling into question the robustness of previous SAR studies. Furthermore, the inability of observed counts and iNEXT.3D to estimate β-diversity model coefficients resulted from a systematic, area-related bias in Sørensen similarity estimates. Importantly, MSOMs corrected for these biases in β-diversity assessments, even in suboptimal scenarios. Nonetheless, as estimator performance consistently improved with increasing sampling repetitions, the importance of appropriate sampling effort cannot be understated.

Life on the edge: Considering ecotonal habitat for the conservation of alpine reptile metacommunities

Conservation planning focuses on core habitats, often overlooking ecotones, which can hold unrecognised potential for biodiversity conservation. This study focused on ecotonal habitat use in alpine reptile metacommunities, with emphasis on a grassland specialist, the critically endangered alpine she-oak skink, Cyclodomorphus praealtus. Survey transects in grasslands and woodlands in Kosciuszko National Park in the Australian Alps were used to investigate reptile occupancy and richness. Data was analysed using a multi-species occupancy model in relation to (1) distance from nearest grassland to assess grassland specialists' occupancy into woodland areas while accounting for imperfect detection, and (2) normalised difference vegetation index (NDVI) to assess the importance of high resource patches. Among the 11 reptile species detected, our hypothesis that grassland specialists would inhabit woodland ecotones was confirmed. The furthest occurrence of C. praealtus from the closest grassland was 41 m with a predicted occupancy of 0.06 (0.004 – 0.169 95 % Bayesian credible intervals) at 100 m. Contrary to conventional edge effect theories, our results revealed no increase in species richness nearer to the woodland ecotone from grasslands or with higher NDVI values. This study underscores the importance of including ecotonal buffers in ecological impact assessments and conservation plans for habitat specialists, that may still use ecotones of adjacent habitats. The findings emphasize the need for broader survey efforts beyond core habitats to capture the distribution of threatened species effectively. Incorporating ecotonal habitats into conservation strategies is crucial, particularly for specialist species whose dynamic use of ecotones may help safeguard them amidst predicted habitat transformation from anthropogenic influences and climate change.

Limited spatiotemporal niche partitioning among mesocarnivores in Gorongosa National Park, Mozambique.

Competition drives community composition and structure in many ecosystems. Spatial and temporal niche partitioning, in which competing species divide the environment in space or time, are mechanisms that may allow for coexistence among ecologically similar species. Such division of resources may be especially important for carnivores in African savannas, which support diverse carnivore assemblages. We used camera traps to explore patterns of spatial and temporal niche partitioning among four mesocarnivore species in Mozambique's Gorongosa National Park: large-spotted genet (Genetta maculata), African civet (Civettictis civetta), honey badger (Mellivora capensis) and marsh mongoose (Atilax paludinosus). We applied a multispecies occupancy model to evaluate spatial partitioning among mesocarnivores and to quantify the environmental factors that affect species-specific habitat use, including relative lion (Panthera leo) activity. We also analyzed the temporal activity overlap of the four focal species. We identified species-specific habitat covariates that influenced detection probabilities but found no evidence of spatial or temporal partitioning among mesocarnivores in the study system. Indeed, we found some evidence for spatial co-occurrence between two of our focal species: African civet and marsh mongoose. There may be limited competition among mesocarnivores in this system, perhaps due to niche and diet differentiation among these species and an abundance of resources. While we found limited evidence that lion activity impacts mesocarnivores, ongoing monitoring of intraguild interactions is vital as apex predator populations recover in the system. This study adds to a growing understanding of African mesocarnivore ecology and highlights the importance of understanding these dynamics for effective multispecies conservation and restoration.

Ecologically informed priors improve Bayesian model estimates of species richness and occupancy for undetected species.

Detection error can bias observations of ecological processes, especially when some species are never detected during sampling. In many communities, the probable identity of these missing species is known from previous research and natural history collections, but this information is rarely incorporated into subsequent models. Here, I present prior aggregation as a method for including information from external sources in Bayesian hierarchical detection models. Prior aggregation combines information from multiple prior distributions, in this case, an ecologically informative, species-level prior, and an uninformative community-level prior. This approach incorporates external information into the model without sacrificing the advantages of modeling species in the context of the community. Using simulated data supplied to a multispecies occupancy model, I demonstrated that prior aggregation improves estimates of (1) metacommunity richness and (2) environmental covariates were associated with species-specific occupancy probabilities. When applied to a dataset of small mammals in Vermont, prior aggregation allowed the model to estimate occupancy correlates of the Eastern cottontail Sylvilagus floridanus, a species observed at several sites in the region but never captured. Prior aggregation can be used to improve the analysis of several important metrics in population and community ecology, including abundance, survivorship, and diversity.

Mammal inventory using camera traps in the Central Forest State Nature Reserve (West of European Russia)

A mammal species inventory by estimating their richness is the first and necessary task of any mammal monitoring programme. This paper presents estimates of species richness of mammals (mostly medium and large body-sized) in the Central Forest State Nature Reserve (European Russia). Based on data collected in 2023 from 55 camera trap locations (19 676 camera days), 59 035 images of wild mammals were obtained. A total of 18 species were recorded. Of these, ten species were representatives of the Carnivora, four – Artiodactyla, two – Rodentia, one – Erinaceomorpha, and one – Lagomorpha. This amounted to 84% of all potentially camera-trapped mammals observed in the Central Forest State Nature Reserve. The relative abundance index (RAI) and naïve occupancy (ψnaive) were calculated for all species. The most common and frequently recorded were Meles meles (RAI = 4.95; ψnaive = 0.96), followed by Ursus arctos (RAI = 4.39; ψnaive = 1) and Lepus timidus (RAI = 4.08; ψnaive = 1), while the most rarely recorded species were Castor fiber (RAI = 0.01; ψnaive = 0.02), Erinaceus europaeus (RAI = 0.02; ψnaive = 0.04), and Lutra lutra (RAI = 0.03; ψnaive = 0.07). Large and medium-sized carnivorous and omnivorous mammal communities were the fastest and most completely captured. According to the constructed single-season multispecies occupancy model with Markov chains Monte Carlo, camera traps failed to record 4–5 more possible species. These species are likely to be Mustela lutreola, M. erminea, and Mustela nivalis, as well as two invasive species, Cervus nippon and Capreolus pygargus. All the captured species were recorded in total in a short period of time, namely from the end of March to the beginning of May during 1869 camera-days. Two of them (Castor fiber and Erinaceus europaeus) were recorded exclusively at this time, and they were not captured further until the end of the year. This emphasises the importance of conducting mammal inventory, with inclusion of the spring season.

Ungulate co-occurrence in a landscape of antagonisms

Protected areas largely now exist as coupled natural-human ecosystems where human activities are increasingly forcing wildlife to adjust behaviors. For many ungulate species that rely on protected areas for their persistence, they must balance these anthropogenic pressures amid natural regulators. Here, we investigated the pressures exerted from humans and livestock, apex predators, and within guild competitors on ungulate co-occurrence patterns in a fragile protected area complex in West Africa. Specifically, we used multi-species occupancy modeling to quantify co-occurrence among four ungulates (Tragelaphus scriptus, Redunca redunca, Kobus kob, Phacochoerus africanus) and applied structural equation models to discern the relative contributions of pressures on co-occurrence patterns. We observed a strong spatial gradient across with higher co-occurrence in the wetter western portion of our ~13,000 km2 study area. Co-occurrence patterns among ungulate dyads ranged from 0.15 to 0.49 with the smallest body sized pair showing highest levels of sympatry, warthog and reedbuck. We found that anthropogenic pressures, namely cattle had the greatest effect in reducing sympatry among wild ungulates more strongly than the presence of African lions that also exhibited negative effects. Humans, hyenas, and competitors showed positive effects on ungulate co-occurrence. In a region of the world ongoing rapid socio-ecological change with increasing threats from climate and environmental instability, protected areas in West Africa represent a major safeguard for wildlife and human livelihoods alike. Our findings highlight the need for effective interventions that focus on large carnivore conservation, habitat restoration, and containment of livestock grazing to promote the coexistence of biodiversity and socio-economic goals within the region.

Forest structure mediates occupancy and extinction of vertebrate prey species on the trailing edge of the boreal forest

Climate change is expected to shift the distributions of global biomes. High latitude biomes, such as the boreal forest, are among the most vulnerable and serve as a bellwether for the effects of climate change on other ecosystems. We examined patterns of occupancy, local extinction, and abundance in a guild of forest-associated vertebrate prey species on the southern margin of the boreal forest in Minnesota (USA). We used multi-season, multi-state, and multi-species occupancy modeling approaches to determine the effects of land cover, forest structural characteristics, and climatic variation on two boreal-associated species, spruce grouse (Canachites canadensis) and snowshoe hare (Lepus americanus), and a forest generalist, ruffed grouse (Bonasa umbellus). Occupancy, abundance, and extinction of spruce grouse was strongly associated with landscape-scale characteristics. In particular, deciduous forest cover may govern their southern range limit. Broadly, forest understory structure played a significant role in occupancy, extinction, and abundance patterns of all three species, with ruffed and spruce grouse generally associated with vegetation density in the lower and mid-canopy layer (5.00–15.00 m) and snowshoe hare associated with density in the shrub layer (1.37–5.00 m) in winter. Co-occurrence varied annually but was greatest in mixed forests during an uncharacteristically warm and snow-sparse year. Climatic variables (winter temperature and snowfall) were associated with extinction probabilities for all three species, but the effect was generally weaker than that of forest structure. Our results suggest that forest management practices that promote dense understory structure may help provide climate refugia for vertebrate prey species in boreal forest ecosystems.

From backyard to backcountry: changes in mammal communities across an urbanization gradient

Abstract Urbanization often results in biodiversity loss and homogenization, but this result is not universal and there is substantial variability in the spatiotemporal effects of urbanization on wildlife across cities and taxa. Areas with lower population and housing density are some of the fastest-growing regions in the western United States; thus, more research in these areas could offer additional insight into the effects of urbanization on wildlife and the potential importance of wild spaces in maintaining a diverse biotic community surrounding developed areas. To address this need, we conducted a study to identify the effects of urbanization (i.e. housing density) on mammals along a housing density gradient from wilderness to suburbia in Missoula, Montana. We deployed 178 motion-activated trail cameras at random sites within urban/suburban, exurban, rural, and wild regions from May to October 2019 to 2020. We identified all mammals &amp;gt;150 g, then evaluated how housing density influenced: (i) occupancy and (ii) species richness using multispecies occupancy models; (iii) relative abundance using Poisson models; and (iv) diel activity patterns using kernel density estimation and logistic regression. Urbanization was the strongest driver of mammal distribution, with a linear decline in mammal species richness as housing density increased. Urbanization also had strong effects on occupancy and detection rates, with larger-bodied mammals generally having stronger negative associations. Overall, mammal relative abundance was highest in suburban regions; however, this effect was largely driven by White-tailed Deer. Natural environmental factors explained most changes in mammal nocturnal activity; however, urbanization strongly affected nocturnality in some species, with Black Bear and White-tailed Deer becoming more nocturnal and Red Fox and Northern Raccoon becoming less nocturnal as housing density increased. While our study confirms that some mammals can live and thrive in developed areas, it emphasizes the importance of maintaining wild areas for those species that cannot.

Frequent prescribed burns reduce mammalian species richness and occurrence in longleaf pine sandhills

Prescribed fire is a critical forest management tool, the frequency and size of which can alter the composition of wildlife communities. In the longleaf pine ecosystem of the southeastern United States, frequent prescribed fire (1–3 year fire interval) is used to replicate natural processes that prevent woody encroachment and transition to alternate states. However, we have little understanding of how different scales and frequencies of fire influence medium and large mammals. To address this knowledge gap, we assessed the homogenizing influence of prescribed fire on mammal community composition at different fire frequencies and scales. We set 110 camera trap grids containing 990 individual camera points across conservation lands in north Florida and the Florida panhandle. We used a Bayesian multi-species occupancy modeling approach to assess the relationship between fire frequency and the occurrence of 11 mammal species across three spatial scales (0.2 ha, 12.57 ha, and 176.71 ha). Species richness was negatively associated with increased burn frequency at all scales and community occurrence was negatively associated with increased burn frequency at the two largest scales. Non-native nine-banded armadillos were negatively associated with increased burn frequency at all scales and non-native feral hogs were negatively associated with increased burn frequency at the two largest scales. Raccoons and opossums, both known nest predators, were negatively associated with increased burn frequency at the two largest scales. Our results indicate that prescribed fire applied at 1–3 year intervals could be used to reduce the occurrence of most non-native mammals and several prolific nest predators in longleaf pine sandhills, particularly at larger scales. However, these perceived benefits must be weighed against the concurrent loss of the ecosystem services and functions native generalist species provide.

Wildlife response to management regime and habitat loss in the Terai Arc Landscape of Nepal

The establishment of protected areas and buffer zones has been widely adopted in many countries to mitigate biodiversity loss. However, in contrast to the growing evidence about the beneficial impacts of protected areas, ecological outcomes of buffer zones have rarely been measured. Here, we use data from a large camera trap survey and multi-species occupancy modelling to assess the effectiveness of different management regimes (Bardia National Park, its buffer zone, and areas outside the buffer zone) at safeguarding wildlife in the Terai Arc Landscape of Nepal. Using areas outside the buffer zone as the counterfactual to compare occurrence probability of 25 mammal species >1 kg, we revealed a positive effect of the national park and the buffer zone on seven and six species, respectively. Three species had greater occurrence probability outside the buffer zone than in the national park, but no species had greater occurrence probability outside the buffer zone than inside the buffer zone. Analysis of species richness indicated that management regime differentially affects species groups. For non-threatened and herbivorous species, the buffer zone performed better than areas outside the buffer zone and similar to, or better than, the national park. However, for threatened species and large animalivores (carnivores and insectivores) the national park outperformed the other management regimes. Our results also suggest that the buffer zone partially mitigated the impacts of habitat loss outside the national park, indicating that management regime may play a role in modulating the effect of agriculture on wildlife in human-dominated landscapes in Nepal.

Evaluating temporal turnover in avian species richness in a Mediterranean semiarid region: Different responses to elevation and forest cover

AbstractAimWhen studying the effects of global change on biodiversity, it is far more common for the effects of climate change and land‐use changes to be assessed separately rather than jointly. However, the effects of land‐use changes in recent decades on species richness in areas affected by climate change have been less studied. We assess the temporal turnover in species richness of an avian community between a historical period and a modern one as a consequence of global change.LocationSemiarid Mediterranean ecosystem (southeastern Spain).MethodWe fitted a hierarchical multispecies occupancy model for each period (1991–1992, and 2012–2017), obtaining avian species‐specific estimates of occupancy probability in relation to environmental covariates (elevation and forest cover). We analyse the relationships between changes in the bird community and environmental variables, analysing the temporal turnover of the species richness and the richness‐based species‐exchange ratio.ResultsThe estimated species richness accounting for detectability was higher than observed species richness, and decreased in the more recent period. Following our hypotheses, we observed a dual pattern of species richness increase associated with different elevations, showing different species turnover rates due to the joint effects of climate change and land‐use change. There is a trend towards greater species richness with higher elevations that is associated with climate change, where the species turnover rate is low. Also, species richness increased towards lower elevations, but with a high turnover rate. The latter can be due to species expansions throughout new habitat configurations in bordering forest systems associated with anthropic land‐use changes.ConclusionsOur study is of great interest to understand the temporal turnover of avian species richness associated with areas experiencing both climate and land‐use change.

Spatial and temporal niche overlap of aardwolves and aardvarks in Serengeti National Park, Tanzania.

Species interactions can influence species distributions, but mechanisms mitigating competition or facilitating positive interactions between ecologically similar species are often poorly understood. Aardwolves (Proteles cristata) and aardvarks (Orycteropus afer) are nocturnal, insectivorous mammals that co-occur in eastern and southern Africa, and knowledge of these species is largely limited to their nutritional biology. We used aardwolf and aardvark detections from 105 remote cameras during 2016-2018 to assess their spatial and temporal niche overlap in the grasslands of Serengeti National Park, Tanzania. Using a multispecies occupancy model, we identified a positive interaction between occupancy probabilities for aardwolves and aardvarks. Slope, proportion of grassland and termite mound density did not affect the occupancy probabilities of either species. The probability of aardwolf, but not aardvark, occupancy increased with distance to permanent water sources, which may relate to predation risk avoidance. Diel activity overlap between aardwolves and aardvarks was high during wet and dry seasons, with both species being largely nocturnal. Aardwolves and aardvarks have an important ecological role as termite consumers, and aardvarks are suggested to be ecosystem engineers. Our results contribute to a better understanding of the spatial and temporal niche of insectivores like aardwolves and aardvarks, suggesting high spatial and temporal niche overlap in which commensalism occurs, whereby aardwolves benefit from aardvark presence through increased food accessibility.

Estimating relative species abundance using fossil data identified to different taxonomic levels

Site‐occupancy modelling is widely used in ecology for understanding species distribution, habitat‐use and community changes but its application is still limited in paleoecology, where incomplete detection is also routine. Here, we make extensive expansions to an earlier multispecies occupancy model used to estimate the dynamics of relative species abundance in fossil communities. These expansions include incorporating counts of individuals at sites, explicitly allowing for the inclusion of specimens assignable to genus – but not species‐level, a situation common in paleontology, and modelling regional presence/absence. We provide simulations to check the performance of this new model, as well as simulations to quantify the benefits of using individual count data versus subsample occupancy data, and model estimates versus face‐value (raw) estimates, respectively. We also provide an empirical case study using occupancy data from a community of marine benthic colonial animals preserved in the Pleistocene of New Zealand. We find that the new model performs well, especially when it comes to recovering relative abundance dynamics and that it is well worth the effort to both collect individual count data and to include individuals unidentified to species‐level in the site‐occupancy modelling framework. This extended model can be widely applied in paleoecological settings and is necessary when both the average and uncertainty values of relative abundance dynamics need to be robustly estimated.

Tropical forest mammal occupancy and functional diversity increase with microhabitat surface area.

Many animal-environment interactions are mediated by the physical forms of the environment, especially in tropical forests, where habitats are structurally complex and highly diverse. Higher structural complexity, measured as habitat surface area, may provide increased resource availability for animals, leading to higher animal diversity. Greater habitat surface area supports increased animal diversity in other systems, such as coral reefs and forest canopies, but it is uncertain how this relationship translates to communities of highly mobile, terrestrial mammal species inhabiting forest floors. We tested the relative importance of forest floor habitat structure, encompassing vegetation and topographic structure, in determining species occupancy and functional diversity of medium to large mammals using data from a tropical forest in the Udzungwa Mountains of Tanzania. We related species occupancies and diversity obtained from a multispecies occupancy model with ground-level habitat structure measurements obtained from a novel head-mounted active remote sensing device, the Microsoft HoloLens. We found that habitat surface area was a significant predictor of mean species occupancy and had a significant positive relationship with functional dispersion. The positive relationships indicate that surface area of tropical forest floors may play an important role in promoting mammal occupancy and functional diversity at the microhabitat scale. In particular, habitat surface area had higher mean effects on occupancy for carnivorous and social species. These results support a habitat surface area-diversity relationship on tropical forest floors for mammals.